Process Description

Recombination and Linkage Groups

Recombination and Linkage Groups calculates a matrix of pairwise recombination rates based on an experimental cross design and clusters the matrix to identify linkage groups for linkage mapping and QTL analysis. Segregation ratios are also calculated for each marker.

What do I need?

Two SAS data sets are required. The first, the input cross file, lists information about the different genetic crosses used in the study. The qtlbcsample_geno.sas7bdat data set, used in the following example, is shown below. This is a wide data set with 300 individuals listed in rows, and the status of individuals for two traits and 36 markers, spanning 3 chromosomes, listed in columns. Markers are formatted as numeric genotypes.

The second required data set is an Annotation Data Set, that lists map information for each of the markers. The qtlbcsample_anno.sas7bdat annotation data set, used in the following example, is shown below. This data set contains 4 columns listing the name and position (in cM) of 36 markers present on three chromosomes.

Both the qtlbcsample_geno.sas7bdat and the qtlbcsample_anno.sas7bdat data sets are located in the Sample Data\QtlMapping directory included with JMP Genomics.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output generated by this process is summarized in a Tabbed report. Refer to the Recombination and Linkage Groups output documentation for detailed descriptions and guides to interpreting your results.